Author Archives: Paddy Lavery

A round up of HUPO 2012, Boston

As mentioned in a previous post, we attended the HUPO 11th Annual World Congress in Boston recently. I was lucky enough to attend so I can share some of the highlights from each day with you. The HUPO council meeting was held on Sunday. Here HUPO shared its vision for the future. One aim is […]

Now you can analyse labelled samples and perform absolute quantification with Progenesis LC-MS

This post refers to Progenesis LC-MS, which has since been superseded by Progenesis QI for proteomics. All of the information described, however, remains relevant. A fuller description of the new product can be found here. Thanks! The Nonlinear Support Team A new publication and software toolkit from the Protein Function Group at the University of […]

Waters and Nonlinear co-develop analysis solutions for large-scale, complex data sets

Following our earlier blog post announcing that we had embarked on a major project with Waters Corporation to supply software as part of their new ‘Omics Research Platform Solution we can bring you a progress update. The formal agreement has been signed and a press release made by Waters Corporation, which was reported the same […]

Proof-of-principle translating discovery proteomics experiments to pre-clinical biomarker verification

A report from the Institute of Medicine has highlighted the on-going challenge of translational proteomics with this line, “transforming the great promise of these new [‘omics] technologies into clinical laboratory tests that can help patients directly has happened more slowly than anticipated.” So, it’s good to be able to share a publication by one of […]

New Omics Research Platform Solution from Waters, powered by Nonlinear Dynamics

Note:This post refers to the TransOmics™ Informatics range of software, which has since been superseded by the Progenesis QI range, which represents the merging of Waters’ TransOmics™ Informatics into Nonlinear Dynamics’ existing Progenesis software. All of the features described, however, remain relevant. A fuller description of the new products can be found here. Thanks! The […]

Label-free LC-MS and 2D gel electrophoresis, complementary approaches to increase proteome coverage

Back in January 2010 I introduced EPSRC CASE award PhD student Andrew Porter, who we sponsor in Prof Gary Black’s lab at Northumbria University. Since then we have been working with them and shared some early results on developing label-free LC-MS methods using a low-resolution ion-trap to study the C. japonicus proteome. The project has […]

Round up of ABRF 2012

The theme of this year’s ABRF meeting was the technology behind the stories, which all good science communications should tell.  Core facility managers and staff, mainly from North America but others from all over the world, came together in Disney’s Contemporary Resort, Orlando, Florida to learn about the technologies available to support them. It was […]

A new version of Progenesis CoMet for metabolomics data analysis

Right now, we have a beta version of Progenesis CoMet v2.0 that we’d love to share with you. The first version was launched back in May 2011 and since then we have been working hard to improve it based on your feedback. It continues to solve the main challenges you face, by giving you confidence […]

Learn how to overcome the problems of quantitative proteomics experiments

Following on from Beth’s last blog post I have more details of our Tutorial Session (T5), which is being held on Tuesday 20th March (4:30pm -5:45pm) at the ABRF 2012 meeting in Orlando, Florida. The title of the tutorial session is Overcoming problems with experiment design for quantitative proteomics and, after a call with all the […]

How can you analyse a mixture of technical and biological replicates in your proteomics experiment?

While this is one of the blog’s more popular posts, it’s worth noting that the recommendations made here should be applied only in situations where you’ve already run your samples. If you’ve yet to run your samples, you can tackle the technical vs. biological replicates issue in a much better way, using an experimental design […]